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Wednesday, January 24, 2018

ATACseq contamination of mycoplasma DNA


  1. Have you thought about using minimap2? It has a Python API (mappy) which you could use to iterate over a fastq file and quickly identify reads which map to one of the potential contaminant genomes.

    1. thanks for the information. I have not used minimap2 yet, fastq_screen seems to be doing OK for me.

  2. Hello, friend! Could you show the changes that were made in config.yaml. I am trying to decontaminate a tryp genome, but I get lost in this procedure. Thx!

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